The rational use and protection of soils and water resources are the most important conditions for the successful intensification of agriculture. Industrial and agricultural enterprises harm the surrounding soils and reservoirs. In order to develop effective soil and water conservation practices, all relationships between individual natural and economic factors must be taken into account. In the article, the authors propose a comprehensive solution to the problem of environmental protection when designing manure removal systems on livestock farms, considering the quantitative relationships between the parameters characterizing the investigated processes. Analysis of the water state in the Yeya River by hydrochemical indicators was performed using a mathematical model. In the study of the ecological system of the Eya River, data from the Hydrometeorological Service and the Kubangipro-Vodkhoz Institute were used. It was concluded that the activities of any livestock farm, any agricultural enterprise of even a small scale, should be accompanied by constant monitoring of the environmental situation with the involvement of scientific achievements, their implementation in the assessment of production and timely adjustment of the results of their work in the direction of preserving the environment, clean soils, reservoirs and air.